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October 18, 2010

Bioconductors:

We are pleased to announce Bioconductor 2.7, consisting of 419 software packages. There are 34 new packages, and many updates and improvements to existing packages. Bioconductor 2.7 is compatible with R 2.12.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS. Visit

http://bioconductor.org

for details and downloads.

Contents

  • Getting Started with Bioconductor 2.7
  • New Software Packages
  • Web Site Updates

Getting Started with Bioconductor 2.7

To install Bioconductor 2.7:

  1. Install R 2.12.0. Bioconductor 2.7 has been designed expressly for this version of R.

  2. Follow the instructions here:

http://bioconductor.org/install/

Please visit http://bioconductor.org for details and downloads.

New Software Packages

There are 34 new packages in this release of Bioconductor.

ADaCGH2

Analysis of aCGH experiments using parallel computing and ff objects

attract

Methods to find gene expression modules representing drivers in Kauffman’s Attractor Landscape

BHC

Bayesian Hierarchical Clustering

BioNet

Functional analysis of biological networks

CGEN

Case-control studies in genetic epidemiology

CoGAPS

Coordinated Gene Activity in Pattern Sets

coRNAi

Analysis of co-knock-down RNAi data

CRImage

Classify cells and calculate tumor cellularity

DEgraph

Two-sample tests on a graph

fabia

Factor Analysis for Bicluster Acquisition

farms

Factor Analysis for Robust Microarray Summarization

gage

Generally Applicable Gene-set Enrichment for Pathway Analysis

GeneGA

Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm

HTSanalyzeR

Network and gene set enrichment analysis pipeline for high throughput screens.

imageHTS

Analysis of high-throughput microscopy-based screens

iSeq

Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models

IsoGeneGUI

A graphical user interface to dose-response analysis of microarray data

les

Identifying Loci of Enhanced Significance in Tiling Microarray Data

LVSmiRNA

LVS normalization for Agilent miRNA data

MBCB

Model-based Background Correction for Beadarray

MEDIPS

MeDIP-Seq data analysis

Mulcom

Differential expression and false discovery rate calculation through multiple comparison

netresponse

Functional network analysis

NTW

Predict gene network using an Ordinary Differential Equation (ODE) based method

NuPoP

Nucleosome positioning prediction

ontoCAT

Ontology parsing

OTUbase

Deals with OTU data

PatientGeneSets

Patient-oriented gene-set analysis

R453Plus1Toolbox

Import and analyze data from Roche’s Genome Sequencer System.

RCytoscape

Display and manipulate graphs in Cytoscape

RDRToolbox

Nonlinear dimension reduction with Isomap and LLE.

RMAPPER

Interface to the MAPPER database of transcription factor binding sites

rnaSeqMap

rnaSeq analyses using xmapcore database

SQUADD

Add-on to Standardized Qualitative Dynamical Systems software for the logical models approach to analysis of complex dynamic systems

Web Site Updates

The Bioconductor web site underwent significant changes during the last release cycle. The web site includes extensive help resources for both users and package developers, in addition to information on package installation. One particularly useful feature in navigating the large numbers of available packages is the updated biocViews widget

http://bioconductor.org/packages/release/BiocViews.html